Examples of HSA

bgu.bio.algorithms.graphs.hsa.HSA

Examples of bgu.bio.algorithms.graphs.hsa.HSA

    };


    TIntArrayList[] alignment = new TIntArrayList[3];


    UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory,false);


    System.out.println("Cost t-s: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    
    
    double ans1 = 0,ans2 = 0;
    
    //reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    double temp = hsaEngine2.computeHSA(t, s);
    ans1 = hsaEngine2.computeHSA(t, sR);
    
    //no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    
    temp = hsaEngine2.computeHSA(t, s);
    hsaEngine2.setFactory(new UnorderedMatcherFactory());
    ans2 = hsaEngine2.computeHSA(t, sR);
    if (!MathOperations.equals(ans1, ans2)){
      System.out.println("Got problem with matchers");
    }
  }

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    };


    TIntArrayList[] alignment = new TIntArrayList[3];


    UnorderedMatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory);


    System.out.println("Cost t-s: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    System.out.println("\nCost s-t: " + hsa.computeHSA(s, t, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    System.out.println("\nCost t-t: " + hsa.computeHSA(t, t, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    System.out.println("\nCost s-s: " + hsa.computeHSA(s, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    long start = System.currentTimeMillis();
    int iters = 10000;
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(t, s);
    }
    System.out.println("\nTime of " + iters + " iterations for t-s: "
        + (System.currentTimeMillis() - start));


    start = System.currentTimeMillis();
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(s, t);
    }
    System.out.println("\nTime of " + iters + " iterations for s-t: "
        + (System.currentTimeMillis() - start));


    start = System.currentTimeMillis();
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(t, t);
    }
    System.out.println("\nTime of " + iters + " iterations for t-t: "
        + (System.currentTimeMillis() - start));


    start = System.currentTimeMillis();
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(s, s);
    }
    System.out.println("\nTime of " + iters + " iterations for s-s: "
        + (System.currentTimeMillis() - start));


    String flowType;

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

  }


  private static void checkTrees(Tree t, CostFunction w, Tree s) {
    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory);


    double cost = hsa.computeHSA(t, s, alignment);
    System.out.println("Cost: " + cost);
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
    System.out.println();


    // checking for pooling problems:
    double currCost;
    int i = 0;
    int iters = 0;
    for (; i < iters; ++i) {
      hsa = new HSA(w, matcherFactory);


      currCost = hsa.computeHSA(t, s);
      if (!MathOperations.equals(cost, currCost)) {
        System.err.println("Different costs at repeated runs: " + cost
            + ", " + currCost);
        break;
      }
    }
    if (i == iters) {
      System.out.println("Repeated runs OK.");
    }


    // checking for symmetry problems:


    alignment = new TIntArrayList[3];
    currCost = hsa.computeHSA(s, t, alignment);
    System.out.println("Cost: " + cost);
    for (int j = 0; j < alignment[0].size(); ++j) {
      System.out.print("(" + alignment[0].get(j) + ","
          + alignment[1].get(j) + "), ");
    }
    System.out.println();


    // checking for pooling problems:
    i = 0;
    for (; i < iters; ++i) {
      hsa = new HSA(w, matcherFactory);


      currCost = hsa.computeHSA(s, t);
      if (!MathOperations.equals(cost, currCost)) {
        System.err.println("Different costs at repeated runs: " + cost
            + ", " + currCost);
        break;
      }

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    smooth.calculateCost(s);


    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    // MatcherFactory matcherFactory = new OrderedMatcherFactory();
    HSA hsa = new HSA(cost, matcherFactory);


    System.out.println("Cost: " + hsa.computeHSA(s, t, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    // System.out.println("\nCost: " + hsa.computeHSA(s, t,alignment));


    System.out.println("\nCost: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    long start = System.currentTimeMillis();
    int iters = 30;
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(t, s);
    }
    System.out.println("\nTime of " + iters + " iterations: "
        + (System.currentTimeMillis() - start));
    String flowType;
//    if (matcherFactory.make(3, 3) instanceof UnorderedBipartiteCavityMatcherMinCostMaxFlow) {

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

  }


  private static void checkTrees(Tree t, CostFunction w, Tree s) {
    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    HSA hsa = new HSA(w, matcherFactory);


    double cost = hsa.computeHSA(t, s, alignment);
    System.out.println("Cost: " + cost);
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }
    System.out.println();


    // checking for pooling problems:
    double currCost;
    int i = 0;
    int iters = 0;
    for (; i < iters; ++i) {
      hsa = new HSA(w, matcherFactory);


      currCost = hsa.computeHSA(t, s);
      if (!MathOperations.equals(cost, currCost)) {
        System.err.println("Different costs at repeated runs: " + cost
            + ", " + currCost);
        break;
      }
    }
    if (i == iters) {
      System.out.println("Repeated runs OK.");
    }


    // checking for symmetry problems:


    alignment = new TIntArrayList[3];
    currCost = hsa.computeHSA(s, t, alignment);
    System.out.println("Cost: " + cost);
    for (int j = 0; j < alignment[0].size(); ++j) {
      System.out.print("(" + alignment[0].get(j) + ","
          + alignment[1].get(j) + "), ");
    }
    System.out.println();


    // checking for pooling problems:
    i = 0;
    for (; i < iters; ++i) {
      hsa = new HSA(w, matcherFactory);


      currCost = hsa.computeHSA(s, t);
      if (!MathOperations.equals(cost, currCost)) {
        System.err.println("Different costs at repeated runs: " + cost
            + ", " + currCost);
        break;
      }

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    smooth.calculateCost(s);


    TIntArrayList[] alignment = new TIntArrayList[3];
    MatcherFactory matcherFactory = new UnorderedMatcherFactory();
    // MatcherFactory matcherFactory = new OrderedMatcherFactory();
    HSA hsa = new HSA(cost, matcherFactory);


    System.out.println("Cost: " + hsa.computeHSA(s, t, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    // System.out.println("\nCost: " + hsa.computeHSA(s, t,alignment));


    System.out.println("\nCost: " + hsa.computeHSA(t, s, alignment));
    for (int i = 0; i < alignment[0].size(); ++i) {
      System.out.print("(" + alignment[0].get(i) + ","
          + alignment[1].get(i) + "), ");
    }


    long start = System.currentTimeMillis();
    int iters = 30;
    for (int i = 0; i < iters; ++i) {
      hsa.computeHSA(t, s);
    }
    System.out.println("\nTime of " + iters + " iterations: "
        + (System.currentTimeMillis() - start));
    String flowType;
    // if (matcherFactory.make(3, 3) instanceof

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    smooth.calculateCost(sR);


    double ans1 = 0, ans2 = 0;


    // reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(),
        true);
    hsaEngine2.computeHSA(t, s);
    ans1 = hsaEngine2.computeHSA(t, sR);


    // no reuse
    hsaEngine2 = new HSA(1, 1, cost, new UnorderedMatcherFactory(), true);


    hsaEngine2.computeHSA(t, s);
    hsaEngine2.setFactory(new UnorderedMatcherFactory());
    ans2 = hsaEngine2.computeHSA(t, sR);
    Assert.assertEquals("Got a problem with the matchers", true,
        MathOperations.equals(ans1, ans2));
  }

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    smooth.calculateCost(s);


    double ans1 = 0, ans2 = 0;


    // reuse
    HSA hsaEngine = new HSA(1, 1, cost, new OrderedMatcherFactory(), true);


    pruneRooted.calculateCost(t);
    pruneRooted.calculateCost(s);
    ans1 = hsaEngine.computeHSA(t, s);


    pruneUnrooted.calculateCost(t);
    pruneUnrooted.calculateCost(s);
    TIntArrayList[] tb = new TIntArrayList[3];
    ans2 = hsaEngine.computeHSA(t, s, tb);
    for (int i = 0; i < tb[0].size(); i++) {
      System.out.println(tb[0].getQuick(i) + " -> " + tb[1].getQuick(i));
    }
    Assert.assertEquals("Should be unrooted alignment", false,
        MathOperations.equals(ans1, ans2));

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Examples of bgu.bio.algorithms.graphs.hsa.HSA

    }
  
    double ans1 = 0, ans2 = 0;


    // reuse
    HSA hsaEngine2 = new HSA(1, 1, cost, new OrderedMatcherFactory(),
        true);
    TIntArrayList[] trace = new TIntArrayList[3];
    ans1 = hsaEngine2.computeHSA(t, t, trace);


    Assert.assertEquals("trace should be the same", trace[0], trace[1]);
    ans2 = hsaEngine2.computeHSA(t, trace);
    
    System.out.println(ans1);
    System.out.println(ans2);


    Assert.assertEquals(

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